diff options
Diffstat (limited to 'gn3/db/traits.py')
| -rw-r--r-- | gn3/db/traits.py | 48 |
1 files changed, 29 insertions, 19 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 7994aef..338b320 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,6 +1,5 @@ """This class contains functions relating to trait data manipulation""" import os -import MySQLdb from functools import reduce from typing import Any, Dict, Union, Sequence @@ -111,7 +110,6 @@ def get_trait_csv_sample_data(conn: Any, def update_sample_data(conn: Any, #pylint: disable=[R0913] - trait_name: str, strain_name: str, phenotype_id: int, @@ -204,25 +202,30 @@ def delete_sample_data(conn: Any, "AND Strain.Name = \"%s\"") % (trait_name, phenotype_id, str(strain_name))) - strain_id, data_id = cursor.fetchone() - cursor.execute(("DELETE FROM PublishData " + # Check if it exists if the data was already deleted: + if _result := cursor.fetchone(): + strain_id, data_id = _result + + # Only run if the strain_id and data_id exist + if strain_id and data_id: + cursor.execute(("DELETE FROM PublishData " "WHERE StrainId = %s AND Id = %s") - % (strain_id, data_id)) - deleted_published_data = cursor.rowcount - - # Delete the PublishSE table - cursor.execute(("DELETE FROM PublishSE " - "WHERE StrainId = %s AND DataId = %s") % - (strain_id, data_id)) - deleted_se_data = cursor.rowcount - - # Delete the NStrain table - cursor.execute(("DELETE FROM NStrain " - "WHERE StrainId = %s AND DataId = %s" % - (strain_id, data_id))) - deleted_n_strains = cursor.rowcount - except Exception as e: #pylint: disable=[C0103, W0612] + % (strain_id, data_id)) + deleted_published_data = cursor.rowcount + + # Delete the PublishSE table + cursor.execute(("DELETE FROM PublishSE " + "WHERE StrainId = %s AND DataId = %s") % + (strain_id, data_id)) + deleted_se_data = cursor.rowcount + + # Delete the NStrain table + cursor.execute(("DELETE FROM NStrain " + "WHERE StrainId = %s AND DataId = %s" % + (strain_id, data_id))) + deleted_n_strains = cursor.rowcount + except Exception as e: #pylint: disable=[C0103, W0612] conn.rollback() raise MySQLdb.Error conn.commit() @@ -255,6 +258,13 @@ def insert_sample_data(conn: Any, #pylint: disable=[R0913] (strain_name,)) strain_id = cursor.fetchone() + # Return early if an insert already exists! + cursor.execute("SELECT Id FROM PublishData where Id = %s " + "AND StrainId = %s", + (data_id, strain_id)) + if cursor.fetchone(): # This strain already exists + return (0, 0, 0) + # Insert the PublishData table cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)" "VALUES (%s, %s, %s)"), |